feat(plotly): implement tree-phylogenetic

plots/tree-phylogenetic/implementations/plotly.py

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+""" pyplots.ai
+tree-phylogenetic: Phylogenetic Tree Diagram
+Library: plotly 6.5.0 | Python 3.13.11
+Quality: 92/100 | Created: 2025-12-31
+"""
+
+import plotly.graph_objects as go
+
+
+# Primate phylogenetic tree based on mitochondrial DNA divergence
+# Newick format: ((((Human:0.1,Chimpanzee:0.1):0.05,Gorilla:0.15):0.1,Orangutan:0.25):0.15,Gibbon:0.4);
+
+# Species and their evolutionary distances from root
+species = ["Human", "Chimpanzee", "Gorilla", "Orangutan", "Gibbon"]
+
+# Cumulative distances from root (calculated from tree topology)
+# Root -> African_ape (0.15) -> HCG_ancestor (0.1) -> HC_ancestor (0.05) -> Human/Chimp (0.1)
+distances_from_root = {
+    "Human": 0.15 + 0.1 + 0.05 + 0.1,  # 0.4
+    "Chimpanzee": 0.15 + 0.1 + 0.05 + 0.1,  # 0.4
+    "Gorilla": 0.15 + 0.1 + 0.15,  # 0.4
+    "Orangutan": 0.15 + 0.25,  # 0.4
+    "Gibbon": 0.4,  # 0.4
+}
+
+# Internal node positions (x = distance from root)
+internal_x = {"Root": 0.0, "African_ape": 0.15, "HCG_ancestor": 0.25, "HC_ancestor": 0.30}
+
+# Y positions for species (leaf nodes)
+species_y = {"Human": 5, "Chimpanzee": 4, "Gorilla": 3, "Orangutan": 2, "Gibbon": 1}
+
+# Y positions for internal nodes (average of children)
+internal_y = {
+    "HC_ancestor": (species_y["Human"] + species_y["Chimpanzee"]) / 2,
+    "HCG_ancestor": (species_y["Human"] + species_y["Chimpanzee"] + species_y["Gorilla"]) / 3,
+    "African_ape": (species_y["Human"] + species_y["Chimpanzee"] + species_y["Gorilla"] + species_y["Orangutan"]) / 4,
+    "Root": 3,
+}
+
+# Build edges for rectangular phylogram
+edge_x = []
+edge_y = []
+
+# Tree structure connections (child, parent)
+connections = [
+    ("Human", "HC_ancestor"),
+    ("Chimpanzee", "HC_ancestor"),
+    ("HC_ancestor", "HCG_ancestor"),
+    ("Gorilla", "HCG_ancestor"),
+    ("HCG_ancestor", "African_ape"),
+    ("Orangutan", "African_ape"),
+    ("African_ape", "Root"),
+    ("Gibbon", "Root"),
+]
+
+# Create edge traces for rectangular phylogram
+for child, parent in connections:
+    # Get child position
+    child_x = distances_from_root[child] if child in species else internal_x[child]
+    child_y = species_y[child] if child in species else internal_y[child]
+
+    # Get parent position
+    parent_x = internal_x[parent]
+    parent_y = internal_y[parent]
+
+    # Horizontal line from child to parent x position
+    edge_x.extend([child_x, parent_x, None])
+    edge_y.extend([child_y, child_y, None])
+
+    # Vertical line at parent x position
+    edge_x.extend([parent_x, parent_x, None])
+    edge_y.extend([child_y, parent_y, None])
+
+# Create figure
+fig = go.Figure()
+
+# Add branch lines (edges)
+fig.add_trace(
+    go.Scatter(
+        x=edge_x, y=edge_y, mode="lines", line={"color": "#306998", "width": 3}, hoverinfo="skip", showlegend=False
+    )
+)
+
+# Add leaf nodes (species)
+leaf_x = [distances_from_root[s] for s in species]
+leaf_y = [species_y[s] for s in species]
+
+fig.add_trace(
+    go.Scatter(
+        x=leaf_x,
+        y=leaf_y,
+        mode="markers+text",
+        marker={"size": 18, "color": "#FFD43B", "line": {"width": 2, "color": "#306998"}},
+        text=species,
+        textposition="middle right",
+        textfont={"size": 20, "color": "#333333"},
+        hovertemplate="%{text}<br>Distance: %{x:.2f}<extra></extra>",
+        showlegend=False,
+    )
+)
+
+# Add internal nodes
+internal_nodes_x = list(internal_x.values())
+internal_nodes_y = [internal_y.get(n, 3) for n in internal_x.keys()]
+internal_labels = list(internal_x.keys())
+
+fig.add_trace(
+    go.Scatter(
+        x=internal_nodes_x,
+        y=internal_nodes_y,
+        mode="markers",
+        marker={"size": 12, "color": "#306998", "symbol": "circle"},
+        hovertemplate="%{text}<br>Distance: %{x:.2f}<extra></extra>",
+        text=internal_labels,
+        showlegend=False,
+    )
+)
+
+# Add scale bar
+scale_bar_y = 0.3
+scale_bar_length = 0.1
+fig.add_trace(
+    go.Scatter(
+        x=[0, scale_bar_length],
+        y=[scale_bar_y, scale_bar_y],
+        mode="lines",
+        line={"color": "#333333", "width": 3},
+        showlegend=False,
+        hoverinfo="skip",
+    )
+)
+
+# Scale bar label
+fig.add_annotation(
+    x=scale_bar_length / 2,
+    y=scale_bar_y - 0.15,
+    text="0.1 substitutions/site",
+    showarrow=False,
+    font={"size": 16, "color": "#333333"},
+)
+
+# Update layout
+fig.update_layout(
+    title={
+        "text": "Primate Evolution · tree-phylogenetic · plotly · pyplots.ai",
+        "font": {"size": 28, "color": "#333333"},
+        "x": 0.5,
+        "xanchor": "center",
+    },
+    xaxis={
+        "title": {"text": "Evolutionary Distance (substitutions per site)", "font": {"size": 22}},
+        "tickfont": {"size": 18},
+        "range": [-0.05, 0.55],
+        "showgrid": True,
+        "gridwidth": 1,
+        "gridcolor": "rgba(0,0,0,0.1)",
+        "zeroline": False,
+    },
+    yaxis={
+        "title": {"text": "", "font": {"size": 22}},
+        "tickfont": {"size": 18},
+        "range": [0, 6],
+        "showticklabels": False,
+        "showgrid": False,
+        "zeroline": False,
+    },
+    template="plotly_white",
+    plot_bgcolor="white",
+    paper_bgcolor="white",
+    margin={"l": 80, "r": 150, "t": 100, "b": 100},
+    showlegend=False,
+)
+
+# Add clade annotations
+fig.add_annotation(
+    x=0.32,
+    y=4.5,
+    text="Hominini",
+    showarrow=True,
+    arrowhead=2,
+    arrowsize=1,
+    arrowwidth=2,
+    arrowcolor="#888888",
+    ax=40,
+    ay=0,
+    font={"size": 16, "color": "#555555", "style": "italic"},
+)
+
+fig.add_annotation(
+    x=0.27,
+    y=3.8,
+    text="Homininae<br>(African Apes)",
+    showarrow=True,
+    arrowhead=2,
+    arrowsize=1,
+    arrowwidth=2,
+    arrowcolor="#888888",
+    ax=50,
+    ay=-20,
+    font={"size": 16, "color": "#555555", "style": "italic"},
+)
+
+fig.add_annotation(
+    x=0.17,
+    y=2.8,
+    text="Hominidae<br>(Great Apes)",
+    showarrow=True,
+    arrowhead=2,
+    arrowsize=1,
+    arrowwidth=2,
+    arrowcolor="#888888",
+    ax=50,
+    ay=-30,
+    font={"size": 16, "color": "#555555", "style": "italic"},
+)
+
+# Save outputs
+fig.write_image("plot.png", width=1600, height=900, scale=3)
+fig.write_html("plot.html", include_plotlyjs="cdn")

plots/tree-phylogenetic/metadata/plotly.yaml

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+library: plotly
+specification_id: tree-phylogenetic
+created: '2025-12-31T13:53:32Z'
+updated: '2025-12-31T14:01:02Z'
+generated_by: claude-opus-4-5-20251101
+workflow_run: 20620332029
+issue: 3070
+python_version: 3.13.11
+library_version: 6.5.0
+preview_url: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/plotly/plot.png
+preview_thumb: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/plotly/plot_thumb.png
+preview_html: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/plotly/plot.html
+quality_score: 92
+review:
+  strengths:
+  - Excellent use of Plotly annotation system with arrows to label taxonomic clades
+  - Scientifically accurate primate phylogeny with correct topology and plausible
+    branch lengths
+  - Clean rectangular phylogram layout with proportional branch lengths
+  - Scale bar with proper units enhances scientific communication
+  - Interactive hover tooltips showing species name and evolutionary distance
+  - Appropriate colorblind-safe color scheme (Python blue/yellow)
+  weaknesses:
+  - Grid lines extend into the tree area which could be cleaner
+  - No legend present, though this is standard for phylogenetic trees